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PostPosted: Wed Aug 29, 2012 9:40 am 
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Joined: Wed Aug 29, 2012 6:02 am
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Respected Sir,
I am novice to the autodock.I want to use 1TUB as receptor.I removed all hetatoms.
Then I tried to add hydrogen It shows some non bonded atoms ( hydrogen and carbon).
When I tried to show cartoon representation of receptor it's become distorted and not seem at all good.


To avoid these I added hydrogen through Pymol, and then make pdbqt file from it.
I found two spurius Apartic acid .
1) one with the single non polar carbon beta hydrogen Asp acid residue.

2)one asp with OH atoms..

ATOM 4889 HN ASP B 76 -97.221 47.335 -21.317 1.00 20.00 0.163 HD
ATOM 4890 N ASP B 76 -96.566 46.894 -20.687 1.00 20.00 -0.347 N
ATOM 4891 CA ASP B 76 -97.084 45.852 -19.925 1.00 20.00 0.168 C
ATOM 4892 C ASP B 76 -96.420 44.599 -20.281 1.00 20.00 0.136 C
ATOM 4893 O ASP B 76 -96.361 43.715 -19.278 1.00 20.00 -0.348 OA
ATOM 4894 HO ASP B 76 -95.930 42.901 -19.509 1.00 0.00 0.219 HD
ATOM 4895 CB ASP B 76 -98.567 45.825 -20.176 1.00 20.00 0.146 C
ATOM 4896 CG ASP B 76 -99.200 47.074 -19.723 1.00 20.00 0.174 C
ATOM 4897 OD1 ASP B 76 -98.586 47.752 -18.898 1.00 20.00 -0.648 OA
ATOM 4898 OD2 ASP B 76 -100.295 47.384 -20.195 1.00


I also find that Met residue also has spurius extra hydrogen atom..

When I run Autogrid4 from terminal ...
I get a lot of warnings like

Found an H-bonding atom with three bonded atoms, atom serial number.....

When I check I these atoms manually I not found any thing as mentioned in warnings..



I am in a lot of confusions ....


So please help me in these respect ..

Thank you in advance


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PostPosted: Thu Feb 06, 2014 12:32 am 
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Joined: Mon Feb 03, 2014 10:41 pm
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I have the same problem. How can i solve it????

Found an H-bonding atom with three bonded atoms, atom
serial number 479

Found an H-bonding atom with three bonded atoms, atom
serial number 888
Found an H-bonding atom with three bonded atoms, atom
serial number 889


what is this ://


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